I would like to separate the two fractions so as to probe for the presence of the protein of my interest in the different fractions.
If you looking to do a proteomics study and you want a cell fractionation technique, here is an article that may be of use to you for your study.
However, I have never heard of a direct method for separating Euchromatin and Heterochromatin.
If necessary, consult others in your department
Thanks Michael for the article. I recently read an article describing the separation of Euchromatin from Heterochromatin using MNase digestion. Thus I wanted to have more ideas before choosing which protocol to choose.
@Maina, if your are looking for protocols that utilizes MNase digestion, attached are 2 that may help you
http://atm.skkumed.ac.kr/protocol/Micrococcal%20Nuclease%20Analysis.pdf
http://www.abcam.com/ps/pdf/protocols/N-ChIP.pdf
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